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Tropical animal health and production2021; 53(3); 334; doi: 10.1007/s11250-021-02776-2

Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers.

Abstract: We investigated the genetic diversity and population genetic structure of six morphologically distinct Ethiopian donkey populations using 12 equine microsatellite markers. The donkey populations were Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI). Blood samples were collected from 180 genetically unrelated donkeys (30 individuals per population). Population genetic diversity estimates showed that total number and mean number of observed alleles, average observed and expected heterozygosity were 94, 5.208 ± 0.0229, 0.555 ± 0.023 and 0.588 ± 0.022, respectively. Highly significant deficiency in heterozygote was detected within the overall samples (F = 0.055 ± 0.021; P < 0.001). Though highly significant (P < 0.001), heterozygote deficiency within populations relative to total population was moderate (F = 0.046 ± 0.016), suggesting a higher diversity within the populations (95.4%) than between populations. Various genetic distance estimation methods produced a similar topology of un-rooted dendrograms that grouped the overall Ethiopian donkeys into lowland (Ogaden, Omo and Sinnar) and highland (Abyssinian, Afar and Hararghe) genetic lineages. Likewise, Bayesian clustering analysis produced a similar pattern of clustering that was highly concordant with traditional donkey classification systems in Ethiopia.
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Publication Date: 2021-05-20 PubMed ID: 34018049DOI: 10.1007/s11250-021-02776-2Google Scholar: Lookup
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Summary

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This study explores the genetic diversity and structure of six separate Ethiopian donkey populations using equine microsatellite markers. The findings show a significant genetic variation within the populations rather than between them, and it also demonstrates that these populations can be grouped into lowland and highland genetic lineages.

Genetic Diversity Investigation

  • The researchers examined six different Ethiopian donkey populations: Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI).
  • To do this, they collected blood samples from 180 donkeys, making sure none of them were related. That means 30 samples were taken from each population’s donkeys.
  • They used 12 equine microsatellite markers to assess the genetic diversity and population genetic structure. These markers are sections of DNA that have sequences that repeat. They are used to determine genetic diversity because they often vary greatly among individuals.

Population Genetic Diversity Estimates

  • The results showed that a total of 94 alleles were found with a mean number of observed alleles of 5.208 ± 0.0229.
  • The average observed heterozygosity was 0.555 ± 0.023, indicating a fair amount of genetic diversity, and the expected heterozygosity was 0.588 ± 0.022.
  • There was a deficiency in heterozygote within the overall samples which was highly significant (F = 0.055 ± 0.021; P < 0.001). This means they found fewer heterozygotes than expected.

Population Genetic Structure

  • Although there was a moderate heterozygote deficiency within populations relative to the total population (F = 0.046 ± 0.016), it was highly significant. This suggests that there was higher diversity within donkey populations (95.4%) than between them.
  • When the genetic distances were estimated using various methods, a similar pattern emerged, dividing the Ethiopian donkeys into two genetic lineages: lowland (comprising Ogaden, Omo and Sinnar) and highland (Abyssinian, Afar and Hararghe).
  • This division was corroborated by Bayesian clustering analysis, a statistical method to infer population structure.
  • The clustering was in line with traditional donkey classification systems in Ethiopia.

This research indicates a considerably rich genetic diversity within rather than between the examined Ethiopian donkey populations. The findings give weight to the traditional classification methods and could have implications for the conservation of these animals.

Cite This Article

APA
Kefena E, Rosenbom S, Beja-Pereira A, Kurtu MY, Han JL, Dessie T. (2021). Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers. Trop Anim Health Prod, 53(3), 334. https://doi.org/10.1007/s11250-021-02776-2

Publication

Tropical animal health and production
ISSN: 1573-7438
NlmUniqueID: 1277355
Country: United States
Language: English
Volume: 53
Issue: 3
Pages: 334

Researcher Affiliations

Kefena, E
  • Department of Animal Genetics and Breeding, Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia. kefenaol@yahoo.com.
Rosenbom, S
  • Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal.
Beja-Pereira, A
  • Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal.
  • Department of Geosciences, Environment and Spatial Planning (DGAOT), Faculty of Sciences, University of Porto, Rua Campo Alegre 687, 4169-007, Porto, Portugal.
Kurtu, M Yusuf
  • Department of Animal and Range Sciences, Haramaya University, P.O. Box 38, Dire Dawa, Ethiopia.
Han, J L
  • CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China.
  • Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia.
Dessie, T
  • Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia.

MeSH Terms

  • Animals
  • Bayes Theorem
  • Equidae / genetics
  • Ethiopia
  • Genetic Variation
  • Genetics, Population
  • Horses / genetics
  • Microsatellite Repeats
  • Phylogeny

Grant Funding

  • PTDC/BIA-BDE/64111/2006 / Portuguese Foundation for Science (FCT)
  • Unknown / German Academic Exchange Service (DAAD)

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Citations

This article has been cited 4 times.
  1. Wang T, Liu Z, Shi X, Zhang Z, Li Y, Huang B, Ren W, Wang X, Wang C, Chai W. An investigation of genetic diversity in three Dezhou donkey original breeding farms. Sci Rep 2023 Jul 11;13(1):11203.
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  2. Wang Y, Hua X, Shi X, Wang C. Origin, Evolution, and Research Development of Donkeys. Genes (Basel) 2022 Oct 25;13(11).
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  3. Zhu Q, Khan MZ, Jing Y, Geng M, Zhang X, Zheng Y, Cao X, Peng Y, Wang C. The Donkey Genome: From Evolutionary Insights to Sustainable Breeding Strategies. Animals (Basel) 2025 Dec 29;16(1).
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  4. Paul S, Shahar N, Seifan M, Bar-David S. An experimental design for obtaining DNA of a target species and its diet from a single non-invasive genetic protocol. Ecol Evol 2023 Oct;13(10):e10616.
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